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Title: A composite linkage map from the combination of three crosses made from commercial clones of cacao, T. cacao L.

item Brown, James
item Sautter, Robert
item Tondo, Cecile
item Borrone, James
item Kuhn, David
item Schnell Ii, Raymond

Submitted to: Tropical Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/14/2007
Publication Date: 4/22/2008
Citation: Brown, J.S., Sautter, R.T., Tondo, C.T., Borrone, J.W., Kuhn, D.N., Motamayor, J.C., Schnell II, R.J. 2008. A composite linkage map from the combination of three crosses made from commercial clones of cacao, T. cacao L.. Tropical Plant Biology. DOI 10.1007/s12042-008-9011-4

Interpretive Summary: Two new fungal diseases have caused tremendous problems in the South and Central American cacao (Theobroma cacao L.) growing areas during the last fifty years, and a third, more ubiquitous disease, black pod (Phytophthora sp.) exists throughout the world and remains troublesome. These diseases have necessitated the location of genes for resistance and the creation of genomic maps saturated with easily used molecular markers. Techniques currently exist and have been used in cacao to locate such resistance genes in donor clones to be used in transferring resistance, and in greatly accelerating the process of transferring this resistance, as much as is biologically possible for cacao. Cacao, like all tree fruits and forest species, have much longer life cycles than annual crops such as grasses and nightshades (tomatoes, peppers, etc.), therefore these techniques are greatly appreciated when they are able to speed up the process. In this study, the genetic maps produced from three crosses composed using six different parents are studied in detail for stability of marker placement within each map and homogeneity of marker placement, comparing the maps produced from the crosses. The six parents are typical of commercial cocoa breeding clones, which have a rather narrow genetic base. The homogeneity of placement of markers on the maps was quite good, and other studies have indicated similar results, indicating that cocoa is found to maintain a rather stable positioning of its genes when comparing six typical commercial clones. Though six clones constitute a small sample, the narrow genetic base of cocoa, together with the fact that most cocoa clones are not more than approximately one to five generations removed from wild cocoa, explain these findings very well. These genetic markers are used to locate genes for resistance to diseases and for genes for horticultural traits. It can likely be expected, therefore, that a great deal of homology can be expected within commercial cocoa clones for location of important genes. As we reach more widely into wild, less related cocoa for novel genes, this homogeneity may decline, however this will occur slowly, given the long generation time needed for breeding cocoa even with assistance from markers.

Technical Abstract: We report here the construction of the first composite map of cacao made from combining map data from three separate cacao populations. The populations arose from crosses of individual clones, which were typical of current breeding material. Codominant simple sequence repeat markers (SSRs) constitute the majority of markers, the remainder being codominant markers from candidate genes (RGHs). Maps contained a total of 307 markers, and genome lengths spanned the range of 762.4 cM to 898.1 cM, implying nearly complete genomic coverage. Individual maps and the composite map contained 10 major linkage groups, corresponding to the number of cacao chromosomes. JoinMap®V4 software was used for all mapping and marker quality assessment. Very high marker location homogeneity (colinearity) had been reported previously across these maps, therefore integrated maps were easily produced. The maximum likelihood algorithm in JoinMap®V4 was used for one F2 population, capable of placing markers in tight groups with greater precision. The other two F1 populations were mapped using the least squares method. Homogeneity of marker placement among individual maps, the composite map, and the “reference” map was very high. Care was exercised in the creation of individual maps and the composite map to eliminate markers showing difficulty in achieving map placement with acceptable mapping quality parameters. The composite map places more SSRs with higher quality than any other map. We consider the placement of SSRs and RGHs presented here to be the most precise currently existing in cacao.